[Chimera-users] Chimera RMSD

[Elaine Meng]

> From: "Sharyn Endow, Ph.D." <sharyn.endow at duke.edu>
> Subject: Chimera RMSD
> Date: January 23, 2021 at 11:27:17 AM PST
> 
> Thank you for your work in developing Chimera. We are trying to use Chimera RMSD to quantitate twisting of a beta-sheet and would like to know what the syntax is to list rmsd values for specified residues corresponding to a beta-strand, not just for single residues. Is it possible to list these values using RMSD? If so, we would greatly appreciate knowing how to get started.
> 
> Sincerely,
> Sharyn

Hi Sharyn,
You can specify any sets of atoms/residues that you like in the RMSD command, as long as there are equal numbers of atoms in the two sets that you specify (from two different models). They will be paired in the order specified.  We have a command-line "atom specification" syntax for that kind of thing.  There is a longish page with lots of examples here:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

In your case, you may need to specify residue numbers, chain ID, and possibly atom names if you just want to use alpha-carbons or backbone as opposed to all atoms of the residues.  E.g. something like

rmsd #0:12.A,57-63.A #1:14.A,59-65.A

... for all atoms of model 0 residues 12 and 57-63 in chain A vs. all atoms of model 1 residues 14 and 59-65 in chain A.  Or to use CA-only or backbone only:

rmsd #0:12.A,57-63.A at ca #1:14.A,59-65.A at ca
rmsd #0:12.A,57-63.A at n,ca,c,o #1:14.A,59-65.A at n,ca,c,o

Of course the numbers could be the same in the two models, I just was trying to give a more general example.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. the chimera-users at cgl.ucsf.edu address CC'd here is recommended for general Chimera how-to or is-it-possible types of questions